Point cloud was created but none of the 2D products was

I recently processed a project where I flew over a detention pond (with water). This time, I flew the drone right after a storm. The first half of the flight, there was no sun, all overcast, but at mid-mission, the clouds started clearing up and the sun was peaking out intermittently. This caused the images to have different colors (not sure if I described it correctly.) Please view the image below.

Overcast:

Sun was exposed:

To make the matter worse, some photos show the reflection of the sun in the water, like this one here:

Do you think this is the reason for the problem in the question? I'm able to view the point cloud just fine. I can choose to view the point cloud in RGB. And to be clear, I ran the project with the new version 2.0 of D2M. If the problem is indeed because of the image quality, is there anything I could do to prevent this situation in the future, e.g. omit these bad photos, fly another round over the site, pick a better day?